get.oturep change and trim.seqs fix

[mothur.git] / chopseqscommand.h

diff --git a/chopseqscommand.h b/chopseqscommand.h
index 604906425997010d3cfcde2b41b9cdeb6b5a1ae7..dbf4d23b71ebc1302672e66bc65472331117713f 100644 (file)
--- a/chopseqscommand.h
+++ b/chopseqscommand.h
@@ -18,18 +18,26 @@ class ChopSeqsCommand : public Command {
        
        public:
        
-               ChopSeqsCommand(string);        
+               ChopSeqsCommand(string);
+               ChopSeqsCommand();      
                ~ChopSeqsCommand(){};
+               vector<string> getRequiredParameters();
+               vector<string> getValidParameters();
+               vector<string> getRequiredFiles();
+               map<string, vector<string> > getOutputFiles() { return outputTypes; }
                int execute();
                void help();    
                
        private:
                string fastafile, outputDir, keep;
-               bool abort, countGaps;
+               bool abort, countGaps, Short;
                int numbases;
+               vector<string> outputNames;
+               map<string, vector<string> > outputTypes;
                
                string getChopped(Sequence);
                
+               
 };
 
 #endif